The Optimum Communication Spanning Tree Problem : properties, models and algorithms

For a given cost matrix and a given communication requirement matrix, the OCSTP is defined as finding a spanning tree that minimizes the operational cost of the network. OCST can be used to design of more efficient communication and transportation networks, but appear also, as a subproblem, in hub location and sequence alignment problems. This thesis studies several mixed integer linear optimization formulations of the OCSTP and proposes a new one. Then, an efficient Branch & Cut algorithm derived from the Benders decomposition of one of such formulations is used to successfully solve medium-sized instances of the OCSTP. Additionally, two new combinatorial lower bounds, two new heuristic algorithms and a new family of spanning tree neighborhoods based on the Dandelion Code are presented and tested.Postprint (published version

Prüfer-Karagül algorithm: A novel approach for travelling salesman problem

Kombinatoryal optimizasyon alanında temel bir model olduğu için literatürde oldukça yaygın çalışılan gezgin satıcı probleminin etkin ve hızlı çözümü için yeni sezgisel yöntemler geliştirilmesine devam edilmektedir. Bu çalışmada, gezgin satıcı problemi için Prüfer-Karagül adı verilen yeni bir yapısal çözüm yaklaşımı önerilmiştir. Önerilen yöntemin performansını değerlendirmek için literatürde yaygın olarak kullanılan gezgin satıcı test problemleri ile analizler yapılmıştır. Yapılan testler sonucunda elde edilen en iyi çözümler optimal çözümden %2, ortalama çözüm değerleri ise %2,50 sapma göstermiştir. Sonuç olarak, önerilen yöntem çözüm performansı ve hızı açısından başarılı çözümler üretmektedir

Optimisation of piping network design for district cooling system

A district cooling system (DeS) is a.scheme for centralised cooling energy distribution which takes advantage of economies of scale and load diversity. . A cooling medium (chilled water) is generated at a central refrigeration plant and then supplied to a district area, comprising multiple buildings, through a closed-loop piping circuit. Because of the substantial capital investment involved, an optimal design of the distribution piping . configuration is one of the crucial factors for successful implementation of a district 1'. cooling scheme. Since there. exists an enormous number of different combinations of the piping configuration, it is not feasible to evaluate each individual case using an exhaustive approach. This thesis exammes the problem of determining an optimal distribution piping configuration using a genetic algorithm (GA). In order to estimate the spatial and temporal distribution of cooling loads; the climatic conditions of Hong Kong were investigated and a weather database in the form of a typical meteorological year (TMY) was developed. Detailed thermal modelling of a number of prototypical buildings was carried out to determine benchmark cooling loads. A novel Local Search/Looped Local Search algorithm was developed for finding optimal/near-optimal distribution piping configurations. By means of computational . experiments, it was demonstrated that there is a promising improvement to GA performance by including the Local Search/Looped Local Search algorithm, in terms of both solution quality and computational efficiency. The effects on the search performance of a number of parameters were systematically investigated to establish the most effective settings. In order to illustrate the effectiveness of the Local Search/Looped Local Search algorithm, a benchmark problem - the optimal communication,spanning tree (OCST) was used for comparison. The results showed that the Looped Local Search method developed in this work was an effective tool for optimal network design of the distribution piping system in DCS, as well as for optimising the OCST problem.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Developing new locality results for the Prüfer Code using a remarkable linear-time decoding algorithm

The Prüfer Code is a bijection between the n n−2 trees on the vertex set [1, n] and the n n−2 strings in the set [1, n] n−2 (known as Prüfer strings of order n). Efficient linear-time algorithms for decoding (i.e., converting string to tree) and encoding (i.e., converting tree to string) are well-known. In this paper, we examine an improved decoding algorithm (due to Cho et al.) that scans the elements of the Prüfer string in reverse order, rather than in the usual forward direction. We show that the algorithm runs in linear time without requiring additional data strutures or sorting routines, and is an ‘online ’ algorithm — every time a new string element is read, the algorithm can correctly output an additional tree edge without any knowledge of the future composition of the string. This new decoding algorithm allows us to derive results concerning the ‘locality’ properties of the Prüfer Code (i.e., the effect of making small changes to a Prüfer string on the structure of the corresponding tree). First, we show that mutating the µth element of a Prüfer string (of any order) causes at most µ + 1 edge-changes i

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

Ereignisbasierte Software-Architektur für Verzögerungs- und Unterbrechungstolerante Netze

Continuous end-to-end connectivity is not available all the time, not even in wired networks. Delay- and Disruption-Tolerant Networking (DTN) allows devices to communicate even if there is no continuous path to the destination by replacing the end-to-end semantics with a hop-by-hop store-carry-and-forward approach. Since existing implementations of DTN software suffer from various limitations, this work presents the event-driven software architecture of IBR-DTN, a lean, lightweight, and extensible implementation of a networking stack for Delay- and Disruption-Tolerant Networking. In a comprehensive description of the architecture and the underlying design decisions, this work focuses on eliminating weaknesses of the Bundle Protocol (RFC 5050). One of these is the dependency on synchronized clocks. Thus, this work takes a closer look on that requirement and presents approaches to bypass that dependency for some cases. For scenarios which require synchronized clocks, an approach is presented to distribute time information which is used to adjust the individual clock of nodes. To compare the accuracy of time information provided by each node, this approach introduces a clock rating. Additionally, a self-aligning algorithm is used to automatically adjust the node's clock rating parameters according to the estimated accuracy of the node's clock. In an evaluation, the general portability of the bundle node software is proven by porting it to various systems. Further, a performance analysis compares the new implementation with existing software. To perform an evaluation of the time-synchronization algorithm, the ONE simulator is modified to provide individual clocks with randomized clock errors for every node. Additionally, a specialized testbed, called Hydra, is being developed to test the implementation of the time-synchronization approach in real software. Hydra instantiates virtualized nodes running a complete operating system and provides a way to test real software in large DTN scenarios. Both the simulation and the emulation in Hydra show that the algorithm for time-synchronization can provide an adequate accuracy depending on the inter-contact times.Eine kontinuierliche Ende-zu-Ende-Konnektivität ist nicht immer verfügbar, nicht einmal in drahtgebundenen Netzen. Verzögerungs- und unterbrechungstolerante Kommunikation (DTN) ersetzt die Ende-zu-Ende-Semantik mit einem Hop-by-Hop Store-Carry-and-Forward Ansatz und erlaubt es so Geräten miteinander zu kommunizieren, auch wenn es keinen kontinuierlichen Pfad gibt. Da bestehende DTN Implementierungen unter verschiedenen Einschränkungen leiden, stellt diese Arbeit die ereignisgesteuerte Software-Architektur von IBR-DTN, eine schlanke, leichte und erweiterbare Implementierung eines Netzwerk-Stacks für Verzögerungs- und unterbrechungstolerante Netze vor. In einer umfassenden Beschreibung der Architektur und den zugrunde liegenden Design-Entscheidungen, konzentriert sich diese Arbeit auf die Beseitigung von Schwächen des Bundle Protocols (RFC 5050). Eine davon ist die Abhängigkeit zu synchronisierten Uhren. Daher wirft diese Arbeit einen genaueren Blick auf diese Anforderung und präsentiert Ansätze, um diese Abhängigkeit in einigen Fällen zu umgehen. Für Szenarien die synchronisierte Uhren voraussetzen wird außerdem ein Ansatz vorgestellt, um die Uhren der einzelnen Knoten mit Hilfe von verteilten Zeitinformationen zu korrigieren. Um die Genauigkeit der Zeitinformationen von jedem Knoten vergleichen zu können, wird eine Bewertung der Uhren eingeführt. Zusätzlich wird ein Algorithmus vorgestellt, der die Parameter der Bewertung in Abhängigkeit von der ermittelten Genauigkeit der lokalen Uhr anpasst. In einer Evaluation wird die allgemeine Portabilität der Software zu verschiedenen Systemen gezeigt. Ferner wird bei einer Performance-Analyse die neue Software mit existierenden Implementierungen verglichen. Um eine Evaluation des Zeitsynchronisationsalgorithmus durchzuführen, wird der ONE Simlator so angepasst, dass jeder Knoten eine individuelle Uhr mit zufälligem Fehler besitzt. Außerdem wird eine spezielle Testumgebung namens Hydra vorgestellt um eine echte Implementierung des Zeitsynchronisationsalgorithmus zu testen. Hydra instanziiert virtualisierte Knoten mit einem kompletten Betriebssystem und bietet die Möglichkeit echte Software in großen DTN Szenarien zu testen. Sowohl die Simulation als auch die Emulation in Hydra zeigen, dass der Algorithmus für die Zeitsynchronisation eine ausreichende Genauigkeit in Abhängigkeit von Kontakthäufigkeit erreicht